Figure 1.
Illustration of the two-level model. The first level is represented in A where the gene evolution happens. In B, one can see the transcript phylogeny. The total edge costs of TA and TB are both zero. While this is expected for TB as transcripts t11 and t21 share the same exons, it is not obvious for TA. Transcripts t12 and t31 differ by exon C. However the latter was gained during the evolution from G0 to G12. This event belong to the first level and thus has zero cost in the transcript phylogeny. The dotted line represents the hidden relationship of the new transcript to its ancestor. In the extended model, that link would be revealed.